BackgroundEvidence linking caries in primary dentition and children’s anthropometric measures is contradictory. We aimed to evaluate the prevalence of primary dental caries and its relationship with body mass index (BMI) among 7-9 years old school children in urban Guangzhou, China.MethodsThis cross-sectional study enrolled 32,461 pupils (14,778 girls and 17,683 boys) aged 7-9 years from 65 elementary schools in Guangzhou. Dental caries was detected according to criteria recommended by the World Health Organization (WHO). The total mean decayed, missing or filled teeth (dmft) of primary dentition were assessed. Weight and height were measured and BMI was calculated. Children were classified into underweight, normal weight, overweight and obesity groups by BMI based on Chinese criteria. Z-score of BMI-for-age (BAZ) was calculated by WHO standardized procedure. Multivariable odds ratios (ORs) and 95 % confidence intervals (CIs) were calculated using logistic regression. Restricted cubic spline regression was applied to evaluate the shape of the relationship between BAZ and primary dental caries.ResultsThe prevalence of primary dental caries was 30.7 % in total sample. Regarding dmft values, the mean ± standard deviation (SD) in the combined sample were 1.03 ± 2.05 in boys and 0.93 ± 1.92 in girls. Both indices decreased by age. Compared with normal BMI group, children in overweight and obesity groups have 27 % (OR = 0.73, 95 % CI: 0.66-0.81, P < 0.0001) and 34 % (OR = 0.66, 95 % CI: 0.59-0.74, P < 0.0001) lower odds for the presence of primary dental caries after adjustment for age and gender, respectively. Although in general, increased BAZ was associated with decreased risk of dental caries, full-range BAZ was associated with dental caries in an A-shaped manner with a zenith at around -1.4.ConclusionHigher BMI was associated with lower odds of caries; overweight and obese children were more likely to be primary dental caries free among 7-9 years in Guangzhou, China.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-016-3295-3) contains supplementary material, which is available to authorized users.